[caret-users] problem with border file

Wed Jun 11 08:06:52 CDT 2008

Hi Sofia,

See inline replies below.

Donna

On 06/11/2008 06:45 AM, Sofia Crespi wrote:
> Dear Donna
> unfortunately the  borders  checkbox is selected on the D/C: 
> Overlay/Underlay -
> Surface menu .
>   
So much for the quick fix....
> When I select the Border Page on the D/C I can see tha name of the new 
> borders in the color section but not in the name section..
> I guess this is the problem.....
>   
This is informative:  It suggests that the border colors are fine 
(unless the color is transparent, which I doubt), but that the border 
didn't load or was empty.

If you saved your border, relative to the FLAT map (i.e., with the FLAT 
map in the main window or the FLAT map selected in the Save Data File: 
Border surface file dialog), then this should not happen with you 
relaunch Caret and select this border file.

Can you upload your data directory (if less than a Gigabyte zipped) here:

http://pulvinar.wustl.edu/cgi-bin/upload.cgi

I want to look at the border file in particular, but other files might also offer clues.

> the next time I'll try to design the border and save the resulting
>  borderproj files but what you mean with "we project borders after drawing 
> them ?"
>   
More recent Caret versions have the radio button "Auto Project" (no by 
default); we usually change this to Yes, because then then the border 
will automatically project as soon as you draw it.  If Auto Project is 
set to No, you can manually project by selecting Layers: Borders: 
Project Borders (or Project Fiducial Borders on older versions).

The "projection" process takes each border point and attaches it to the 
closest surface tile.  This is why you can view projected borders on 
multiple surface configurations (fiducial, flat, inflated).  When you 
save a borderproj file, you're saving the border as attached to the 
nearest tile; when you save as border, there is no surface allegiance; 
the points are floating in 2D or 3D space -- perhaps close to the 
surface, perhaps not (kind of like foci in that respect).

I don't think your trouble with the border saving/reloading is due to 
your not projecting; the cause remains elusive.
> thank you
> Sofia
>
> ----- Original Message ----- 
> From: "Donna Dierker" <donna at brainvis.wustl.edu>
> To: "Caret, SureFit, and SuMS software users" 
> <caret-users at brainvis.wustl.edu>
> Sent: Tuesday, June 10, 2008 2:55 PM
> Subject: Re: [caret-users] problem with border file
>
>
>   
>> Hi Sofia,
>>
>> See inline replies below.
>>
>> Donna
>>
>> On 06/10/2008 06:18 AM, Sofia Crespi wrote:
>>     
>>> Hi I have a question.
>>> I've designed some closed border on my flat surface in order to use
>>> them for surface region of interest operation.
>>> More precisely I've daone these operations:
>>> 1.Layers---->Borders---->draw Borders
>>> 2. I've selected a new name, closed boundaries and 2D,
>>>     in the closed border assignement frame-----> Voxels I've selected
>>> Assign voxels within closed borders and +/-1 for the thickness.
>>> 3. I've choosed a color and designed my border on the flat map.
>>> 4.Then I saved the file with a new name as: border file Surface,
>>> border file Volume, Border color file.
>>>
>>> Now I'm able to see the border and if I select the Border Page in the
>>> Dispaly control dialog I can find the name and the color of my new
>>> border. Now I close caret.
>>> If I open caret again and load my spec file, loading also the new
>>> border file already created I cannot display the new border on the
>>> flat map...
>>> why?
>>>       
>> If both the border file Surface and border color files that you saved in
>> step 4 above were selected when you loaded the spec file, then the only
>> other reason I can imagine that you don't see the border on your flat
>> map is that borders are not selected on the D/C: Overlay/Underlay -
>> Surface menu (scroll all the way to the bottom, until you see a borders
>> checkbox); see attached capture, which shows the Borders checkbox
>> toggled on at the bottom of the D/C: Overlay/Underlay - Surface page.
>>
>> Depending on which Caret version you have, this checkbox may or may not
>> be on by default when you load a spec with borders selected.
>>     
>>> I opened the border file Surface just created....
>>> all the other border file come out as *appended* (why since are
>>> different file????) the last one is not appended and I cannot see that
>>> border....
>>>       
>> This is not clear to me.  Perhaps if you uploaded your dataset, I could
>> decipher what you mean.
>>
>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>> It sounds like one or more of the following possibilities might
>> contribute to the confusion:
>>
>> 1. You have multiple border files loaded, which may have borders that
>> intersect/duplicate with one another.
>> 2. When you couldn't see the border upon opening, you tried loading
>> again, resulting in the same borders being loaded twice.
>>
>> I hope this is just a case of the borders not being turned on when you
>> relaunch Caret.
>>     
>>> Please have a look to the doc fiel attached:
>>>       
>> No doc file was attached.
>>     
>>> in yellow I've underlined all the attached file...:
>>> *1* *why the same file "V6 border color " is appended more than 1 time?*
>>>       
>> Something similar to possibilities 1 and 2 occurred wth the bordercolor
>> file.
>>     
>>> *2. the appended file LO-MST-MT is refereed to 3 border That I'm not
>>> able to disply any more..*
>>>       
>> I don't understand this question, but I hope the display problem is
>> resolved by the D/C checkbox.
>>     
>>> *3 the new border V6NEW does not result as appended ??*
>>>       
>> Perhaps it was added after the last save?  I can't think of another
>> plausible explanation.
>>     
>>> where is my error?
>>>       
>> Let's hope the D/C checkbox resolves 90% of your issues.
>>     
>>> can you help me?
>>>       
>> Typically, we project borders after drawing them and save the resulting
>> borderproj files.  This allows you to view the borders on multiple
>> surfaces (e.g., fiducial, inflated).  There are definitely contexts in
>> which border files have distinct advantages, however (e.g., when viewing
>> on surfaces of different mesh / number of nodes than the drawing
>> substrate; when using the 2D/3D coordinates for an outside application).
>>
>> But you clearly state above you are trying to view your borders on the
>> flat map, which is the same surface used for the drawing substrate.
>> Thus, I conclude that this is probably a D/C checkbox not selected issue.
>>     
>>> Thank you in advance
>>>
>>> Sofia Crespi
>>>       
>
>
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